Restriction of SARS-CoV-2 replication by receptor transporter protein 4 (RTP4)

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is subject to restriction by several interferon-inducible host proteins. To identify novel factors that limit replication of the virus, we tested a panel of genes that we found were induced by interferon treatment of primary human monocytes by RNA sequencing. Further analysis showed that one of the several candidates genes tested, receptor transporter protein 4 (RTP4), that had previously been shown to restrict flavivirus replication, prevented the replication of the human coronavirus HCoV-OC43. Human RTP4 blocked the replication of SARS-CoV-2 in susceptible ACE2.CHME3 cells and was active against SARS-CoV-2 Omicron variants. The protein prevented the synthesis of viral RNA, resulting in the absence of detectable viral protein synthesis. RTP4 bound the viral genomic RNA and the binding was dependent on the conserved zinc fingers in the amino-terminal domain. Expression of the protein was strongly induced in SARS-CoV-2-infected mice although the mouse homolog was inactive against the virus, suggesting that the protein is active against another virus that remains to be identified. IMPORTANCE The rapid spread of a pathogen of human coronavirus (HCoV) family member, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), around the world has led to a coronavirus disease 2019 (COVID-19) pandemic. The COVID-19 pandemic spread highlights the need for rapid identification of new broad-spectrum anti-coronavirus drugs and screening of antiviral host factors capable of inhibiting coronavirus infection. In the present work, we identify and characterize receptor transporter protein 4 (RTP4) as a host restriction factor that restricts coronavirus infection. We examined the antiviral role of hRTP4 toward the coronavirus family members including HCoV-OC43, SARS-CoV-2, Omicron BA.1, and BA.2. Molecular and biochemical analysis showed that hRTP4 binds to the viral RNA and targets the replication phase of viral infection and is associated with reduction of nucleocapsid protein. Significant higher levels of ISGs were observed in SARS-CoV-2 mouse model, suggesting the role of RTP4 in innate immune regulation in coronavirus infection. The identification of RTP4 reveals a potential target for therapy against coronavirus infection.

A genome-wide arrayed CRISPR screen identifies PLSCR1 as an intrinsic barrier to SARS-CoV-2 entry that recent virus variants have evolved to resist

“…To provide a thorough perspective on human genes that impact SARS-CoV-2 infection and to place our arrayed CRISPR KO screen results within the context of existing research, we have compiled a table that includes findings from a selection of 67 large-scale ‘omic’ studies related to SARS-CoV-2. This compilation encompasses this study and 25 other functional genetic screens for genes that influence SARS-CoV-2 infection [10–12, 14, 17, 18, 26, 29, 60–76], 24 human genetic studies that correlate certain alleles with severe COVID-19 outcomes [4, 5, 7, 23, 24, 77–95], ten publications detailing SARS-CoV-2 protein interactomes [96–105], six focusing on SARS-CoV-2 RNA interactomes [106–111], and one that examines proteins with altered phosphorylation states in SARS-CoV-2-infected cells [112] (Supp Tables 9-10 for the full, and summary tables, respectively) . This table highlights the depth of research in publications addressing SARS-CoV-2 infection: genes reported in several independent large-scale studies are more credible candidates for biological relevance ( Supp Fig 2 ).…”

“…Several PLSCR1 variants were enriched in a GWAS on severe COVID-19, with a relatively low odds ratio of approximately 1.2 [23, 24]. Considering the complex redundancies within antiviral defenses, from innate immunity featuring multiple effector ISGs that restrict SARS-CoV-2 [9–14, 17, 18], to adaptive immunity [154], the modest odds ratio associated with a single effector ISG not involved in IFN signaling may not be unexpected. However, for these very reasons, the identification of PLSCR1 in the GWAS remains noteworthy.…”

“…Israeli, et al [70]: we used Supplementary Data 1. Kaur, et al [14]: we used the genes labelled in Figure 1. Le Pen et al (this study): we used z-score ≥ 2 for antiviral genes and ≤ 2 for proviral genes, see Unbiased arrayed CRISPR KO Screen analysis section above for more details.…”

“…Most of these studies involved gain-of-function genetic screens, over-expressing individual ISGs. The factors bone marrow stromal cell antigen 2 (BST2), cholesterol 25-hydroxylase (CH25H), lymphocyte antigen 6 family member E (LY6E), 2’-5’-oligoadenylate synthetase 1 (OAS1), and receptor transporter protein 4 (RTP4) were notably identified as SARS-CoV-2 antivirals in these studies [9–14]. One advantage of the gain-of-function approach is that it circumvents potential genetic redundancies between ISGs [15, 16].…”